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UC Berkeley Berkeley Scientific Journal UC Berkeley Berkeley Scientific Journal Title Insights from the JGI User Meeting: Using Genomics to Tackle Environmental Problems Permalink https://escholarship.org/uc/item/92b490h8 Journal Berkeley Scientific Journal, 23(2) ISSN 1097-0967 Authors Harari, Emily Colbert, Matthew Chari, Nikhil Publication Date 2019 Undergraduate eScholarship.org Powered by the California Digital Library University of California INSIGHTS FROM THE JGI USER MEETING: USING GENOMICS TO TACKLE ENVIRONMENTAL PROBLEMS BY EMILY HARARI, MATTHEW COLBERT, AND NIKHIL CHARI Soil microbiology, plant-pathogen interactions, com- putational biology, and big data all converge in the rising field known as genomics, which involves DNA sequencing and analysis to determine the interactions between organisms integral to biological processes.1 The Department of Energy Joint Genomics Institute (JGI) aims to solve problems in renewable energy, eco- system nutrient cycling, and decontamination using genomics techniques.1 BSJ covered the 2019 JGI User Meeting where we had the opportunity to speak with four distinguished scientists working with genomics to tackle issues as wide-ranging as the fate of carbon in soil systems to the discovery of higher-order combina- torial interactions in cells. BSJ spoke with soil micro- biologist Mary Firestone and plant pathologist Mary Wildermuth from UC Berkeley, immunologist Arturo Casadevall from Johns Hopkins, and computational biologist Dan Jacobson from Oak Ridge National Lab- oratory. Our conversations highlighted some of the widely varied genomics research taking place today. From left to right: Dr. Mary Firestone, Dr. Mary Wilder- muth, Dr. Arturo Casadevall, and Dr. Dan Jacobson. SPRING 2019 | Berkeley Scientific Journal 29 Figure 1: Grand Prismatic Spring, Yellowstone National Park.7 Microbial mats give the spring its vivid colors. rofessor Mary Firestone and Professor Wildermuth both fies soil viruses as a “big unknown,” she considers fauna to be a “big Pspoke about their research in plant and soil microbiology known.” Much research has been done to determine the roles of soil on April 4th. Firestone, a renowned soil microbiologist and biogeo- fauna (small Metazoa like nematodes and mites) in making essen- chemist, was the day’s keynote speaker, and discussed her research tial nutrients like N and phosphorus (P) bioavailable to plants, but, in using various genomics techniques to probe the fate of carbon (C) according to Firestone, the relationship between faunal food webs in soil systems. She spent much of her career investigating microbi- and soil C remains under-investigated and “begging for improved al relationships to nutrient cycling, especially nitrogen (N), in soils, molecular tools.” and is more recently diving into C dynamics. Among these tools is a genomics technique called primer quan- In our interview, Firestone explained that “soil microbes, in a lot titative PCR, or qPCR. Faunal quantification has typically been per- of ways, are Mother Earth,” and that they are as “fundamental to life formed by visual identification and direct counting in soils. Howev- on Earth as anything.” Microbes in soil have long been known to be er, Firestone and colleague Javier Ceja-Navarro at Lawrence Berkeley critical players in the decomposition of soil organic matter (SOM) to National Lab found that primer qPCR yields largely similar quanti- 2 carbon dioxide, CO2. But more recently, they have been recognized tative results. Firestone explained how qPCR can make quantifying for their importance in the stabilization of C in soil, from C sorption fauna in soil much easier: “You simply have to take a large sample of to mineral surfaces to the formation of aggregates—clusters of soil soil to encompass faunal diversity, extract the DNA, and use specific particles that bind together and can sequester C within them. primers to do PCR amplification of the barcode that you want to Firestone explained why she chooses to trace each type of DNA quantify. That gave us very, very similar results to the direct counting found in these soil clusters. There has been little research in the soil method, and confirmation that qPCR works quantitatively.” viral genome because soil is a solid matrix—viruses are difficult to Firestone’s research also tackles the impact of arbuscular mycor- filter out and can easily sorb to minerals or organic materials. Con- rhizal fungi (AMF) on soil ecosystems. AMF are unlike most fungi sequently, very little is known about the importance of viruses to soil in that they are not saprotrophs. Where saprotrophs use dead C as ecosystems and nutrient and C cycling. Although Firestone classi- an energy source, AMF are biotrophic, or as Firestone said, “they eat 30 Berkeley Scientific Journal | SPRING 2019 Figure 2: One of Dr. Casadevall’s watercolor paintings. Reprinted with permission. living C by plugging directly into plant roots.” The exchange is mutu- detection probe (for research use) in concert with doctors at the al—AMF also pick up essential nutrients like N and P from the sur- NIH. While contemplating her future options, Wildermuth elected rounding soil and transport them back to plants. Firestone’s recent to travel abroad. “I had always wanted to go to Africa to get more genomics research focuses on what she calls “helper bacteria,” which of a perspective on what I wanted to study,” she said. After teaching associate with AMF. Though Firestone stressed that “this is a story science for two years in Molepolole, Botswana, she returned to the that’s still unraveling,” she believes helper bacteria could work to de- US and worked at the National Center for Atmospheric Research compose organic N into ammonia—a bioavailable form that AMF (NCAR), studying plant gas production and climate change. She can help transport into plants. By 13C-labeling AMF hyphae and trac- ultimately obtained her doctorate in Biochemistry at the University ing which bacteria around the hyphae are picking up 13C, Firestone of Colorado, Boulder, exploring how plants make the reactive gas and her group are working to “establish a direct link between hyphae isoprene. supplying C and bacteria living around them that are consuming it.” In her postdoctoral work at Massachussets General Hospital Despite her strides in soil metagenomics, Firestone stressed that (Harvard Medical School), Wildermuth then expanded her study of there is still much work to be done. “Soil is the most diverse microbial plants to include microbial pathogens, with a special focus on the habitat on Earth,” she explained, but a “very, very small percentage of powdery mildew fungus. “The reason that I love it is that it’s an ob- the soil genome—less than 1%—has been sequenced.” This is largely ligate biotroph, so it can only grow on a living plant,” she said. Pow- because it’s difficult to extract DNA from a solid yet dynamic matrix dery mildew is a fungal plant pathogen characterized by white spots like soil. But Firestone still believes there are “many, many lives of on a plant’s leaves. An individual powdery mildew species can typ- interesting research for young students in this area of research.” Professor Mary Wildermuth also studies plant-microbe inter- actions in soil systems, but her path to the field could not have been more different. While she conducted undergraduate research and “If you go into a hospital today, the graduated with a degree in chemical engineering from Cornell, she microbes you recover from wasn’t sure she wanted to stick with the field. “I realized as a chemical engineer that I was missing biology,” Wildermuth recounted. “From infected individuals look very there, biotech was pretty new, and I realized I didn’t want to go into different from those that would have traditional chemical engineering.” She obtained a position at biotech company Gibco-BRL and helped create the first Hepatitis B DNA been causing disease in the 1900s.” SPRING 2019 | Berkeley Scientific Journal 31 pects of host-microbe interactions that are neglected in models “I often wonder, if Darwin had where all microbes are assumed pathogens. Casadevall wants to tackle the nuances of immunology with a quantitative approach. “If I written On the Origin of Species today, lived in the ancient world, I’d be called part of the cult of Pythagoras,” where would he have published?” he said. He believes that “the mathematics of the system will tell you the degree to which anything is predictable,” and his current collab- oration with biomathematician Aviv Bergman at Yeshiva University turns to dynamical systems as a way to predict trends within biologi- ically infect similar host plants, while different species of powdery cal systems. As Casadevall explained, dynamical systems use a func- mildew can infect different sets of plants. “The spores are windborne, tion to describe the time dependence of a point in space. Rather than and it’s almost all asexually reproduced… and they’ll make them in hold the microbe constant or the host constant, as in most contem- five days to a week,” Wildermuth explained. This makes them a com- porary experimental designs, dynamical systems allow Casadevall mon nuisance. and Bergman to look at the interactions of both organisms over time. Powdery mildew’s interactions with the plant host are what most By analyzing patterns from many simulations, they have concluded fascinate Wildermuth, who likens them to a mass-balance equation. that virulence is an emergent property —a characteristic exhibited of In this interaction, the powdery mildew establishes a feeding struc- a complex system like the host-microbe relationship, rather than an ture in the upper layer of the plant in order to siphon nutrients for individual microbe. Casadevall explained that microbes “hedge their itself. The interaction doesn’t only touch the upper layer though, as bets” by randomly varying their behavior in order to better infect Wildermuth’s lab discovered. “Below those, in the mesophyll cells in their hosts.
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